- Title
- Gene expression, copy number variation and DNA methylation associated with disease outcome in triple negative breast cancer
- Creator
- Pariyar, Mamta
- Relation
- University of Newcastle Research Higher Degree Thesis
- Resource Type
- thesis
- Date
- 2021
- Description
- Research Doctorate - Doctor of Philosophy (PhD)
- Description
- Breast cancer is the most common cancer and the leading cause of death in women worldwide. Triple negative breast cancer (TNBC) is a highly aggressive subtype of breast cancer with a high rate of metastasis, early distant recurrence and it is highly resistant to therapy leading to worse survival than other subtypes of breast cancer. There are no well-established biomarkers that can determine women who will do better and those who are likely to have poorer outcomes, nor are there targeted therapies for this breast cancer subtype. Thus, the identification of prognostic and predictive biomarkers that can determine those women who are likely to have poorer outcomes will enable tailored therapies based on their likelihood of potential disease outcomes and may prevent over- and under-diagnosis. Previous studies from our laboratory have identified genes (ANP32E, DSC2, ANKRD30A and IL6ST) that are specific to TNBC and that are associated with lymph node metastasis (LNmets), the earliest indicator of tumour progression and metastasis to distant sites. Thus, further validation of this result using alternative techniques is required. Additionally, early biomarkers that are associated with lymph node metastasis or with treatment response in TNBC are currently unknown. Thus, this thesis aimed to identify genetic and epigenetics changes in TNBC and their association with clinicopathological features, lymph node metastasis and response to treatment, which may have a prognostic role in the TNBC subpopulation. In Chapter 3, the mRNA expression of ANP32E, DSC2, ANKRD30A and IL6ST was examined in TNBC versus non-TNBC using digital droplet PCR (ddPCR), where they were found to be differentially expressed. Their differential expression was associated with clinicopathological features which may imply their potential role in determining prognosis in TNBC. The expression level of DSC2 and ANP32E proteins was determined using immunohistochemistry (IHC). However, the correlation between mRNA and protein expression levels of these two genes was low which could be due to post transcriptional regulation or due to the sensitivity of protein detection method. In Chapter 4, significant copy number variations (CNVs) in IDCs and LNmets, as well as those associated with LNmets in TNBC were identified and correlated with gene expression profiles. The total list of LNmet associated genes was highly enriched in the GO terms including vi “regulation of complement activation” and “trail binding”. Importantly, of the total list of LNmet associated genes, six (ASPM, KIF14, LEMD1, SNORD113-2, SNORD113-3, SNORD113-4) were identified to contain CNVs and showed a corresponding change in mRNA expression, suggesting that their further validation may lead to promising prognostic markers in TNBC. In Chapter 5, CNVs associated with a pathological complete response (pCR) were identified in two neoadjuvant cohorts- NeoGem and WSG-ADAPT. Several CNVs identified were highly enriched in critical pathways such as “DNA repair”, “cell proliferation” and “cell adhesion”. There was very little overlap of CNVs between the two cohorts implying that the markers associated with treatment response may rely on the specific treatment. However, this needs validation in larger cohorts. Furthermore, in the same two neoadjuvant cohorts, DNA methylation profiles associated with pCR were identified (Chapter 6). Differentially methylated probes (DMPs) and differentially methylated regions (DMRs) distributed across genomic regions as well as outside of the genes were identified. Importantly, several of them were associated with promoter hypermethylation and found to be highly enriched in biological processes such as “DNA binding transcription activity”, “cell junction” and “cytoskeletal protein binding” suggesting their potential role in treatment resistance by abnormally regulating DNA binding activity and cell proliferation pathways. Taken together, this thesis has provided important insights into TNBC aggression by revealing several genetic and epigenetic changes associated with the progression of TNBC from primary tumour to LNmet and those involved in treatment response. Thus, this thesis presents novel concepts for developing prognostic biomarkers for TNBC and these may represent new targeted treatment option in the future.
- Subject
- triple negative breast cancer; copy number variation; DNA methylation; lymph node metastasis
- Identifier
- http://hdl.handle.net/1959.13/1494586
- Identifier
- uon:53830
- Rights
- Copyright 2021 Mamta Pariyar
- Language
- eng
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| Thumbnail | File | Description | Size | Format | |||
|---|---|---|---|---|---|---|---|
| View Details Download | ATTACHMENT01 | Thesis | 14 MB | Adobe Acrobat PDF | View Details Download | ||
| View Details Download | ATTACHMENT02 | Abstract | 423 KB | Adobe Acrobat PDF | View Details Download |